TABLE 2.
Category and locus tag | Gene | COG name | Expression ratio (mixed culture/monoculture) |
|||
---|---|---|---|---|---|---|
3.5 h | 5.5 h | 8 h | 12 h | |||
Folic acid metabolism | ||||||
LBUL_0208 | Dihydroneopterin aldolase | 0.88 | 0.43 | 1.28 | 2.25 | |
LBUL_0209 | GTP cyclohydrolase I | 0.40 | 0.32 | 1.35 | 1.64 | |
LBUL_0210 | Folylpolyglutamate synthase | 0.50 | 0.31 | 1.41 | 1.44 | |
LBUL_0211 | Dihydropteroate synthase and related enzymes | 0.69 | 0.39 | 1.39 | 2.30 | |
LBUL_0212 | NTP pyrophosphohydrolases including oxidative damage repair enzymes | 0.63 | 0.31 | 1.26 | 2.88 | |
LBUL_0660 | Folylpolyglutamate synthase | 0.69 | 0.37 | 0.78 | 4.82 | |
Purine metabolism | ||||||
LBUL_0156 | Phosphoribosylpyrophosphate synthetase | 2.09 | 1.16 | 0.44 | 0.50 | |
LBUL_0246 | IMP dehydrogenase/GMP reductase | 0.24 | 0.30 | 1.27 | 0.05 | |
LBUL_0251 | IMP dehydrogenase/GMP reductase | 2.63 | 0.68 | 1.33 | 0.91 | |
LBUL_0252 | GMP synthase PP-ATPase domain/subunit | 2.32 | 0.94 | 1.57 | 1.60 | |
LBUL_0305 | Phosphoribosylpyrophosphate synthetase | 0.78 | 0.66 | 0.57 | 1.32 | |
LBUL_1330 | Phosphoribosylamine-glycine ligase | 0.99 | 0.37 | 1.18 | 0.06 | |
LBUL_1331 | AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) | 1.21 | 0.43 | 1.23 | 0.05 | |
LBUL_1332 | Folate-dependent phosphoribosylglycinamide formyltransferase PurN | 1.20 | 0.58 | 1.22 | 0.06 | |
LBUL_1333 | Phosphoribosylaminoimidazole (AIR) synthetase | 1.29 | 0.34 | 1.19 | 0.04 | |
LBUL_1334 | Glutamine phosphoribosylpyrophosphate amidotransferase | 1.25 | 0.37 | 1.28 | 0.05 | |
LBUL_1335 | Phosphoribosylformylglycinamidine (FGAM) synthase synthetase domain | 1.66 | 0.46 | 1.18 | 0.07 | |
LBUL_1336 | Phosphoribosylformylglycinamidine (FGAM) synthase glutamine amidotransferase domain | 0.96 | 0.44 | 0.92 | 0.04 | |
LBUL_1337 | Phosphoribosylformylglycinamidine (FGAM) synthase PurS component | 0.89 | 0.61 | 0.81 | 0.03 | |
LBUL_1338 | Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase | 0.83 | 0.64 | 0.88 | 0.03 | |
LBUL_1339 | Adenylosuccinate lyase | 1.79 | 1.78 | 0.85 | 0.17 | |
LBUL_1340 | Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) | 2.05 | 1.90 | 0.92 | 0.10 | |
LBUL_1341 | Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase | 1.96 | 1.55 | 0.57 | 0.14 | |
LBUL_1754 | GMP synthase-glutamine amidotransferase domain | 1.21 | 0.59 | 1.52 | 1.78 | |
str0030 | purC | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 2.74 | 1.15 | 0.27 | 0.10 |
str0031 | purL | Phosphoribosylformylglycinamidine synthase II (FGAM synthetase) | 1.94 | 1.50 | 0.40 | 0.31 |
str0031 | purL | Phosphoribosylformylglycinamidine synthase II (FGAM synthetase) | 1.94 | 1.50 | 0.40 | 0.31 |
str0032 | purF | Amidophosphoribosyltransferase | 1.59 | 1.61 | 0.45 | 0.43 |
str0033 | purM | Phosphoribosylaminoimidazole synthetase | 1.54 | 1.64 | 0.48 | 0.47 |
str0034 | purN | Phosphoribosylglycinamide formyltransferase | 1.47 | 1.60 | 0.50 | 0.48 |
str0035 | purH | Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase | 1.86 | 2.18 | 0.47 | 0.70 |
str0040 | purD | Phosphoribosylamine-glycine ligase | 4.90 | 2.56 | 0.50 | 0.15 |
str0041 | purE | Phosphoribosylaminoimidazole carboxylase catalytic subunit | 5.76 | 4.05 | 0.79 | 0.20 |
str0042 | purK | Phosphoribosylaminoimidazole carboxylase | 5.41 | 3.90 | 0.77 | 0.31 |
str0045 | purB1 | Adenylosuccinate lyase | 2.23 | 2.08 | 0.53 | 0.37 |
str1640 | pflA | Pyruvate-formate lyase activating enzyme | 4.06 | 0.79 | 0.66 | 0.47 |
str1657 | pfl | Pyruvate formate-lyase | 3.03 | 1.38 | 0.97 | 0.76 |
BCAA metabolism | ||||||
LBUL_0077 | l-2-Hydroxyisocaproate dehydrogenase | 0.64 | 0.86 | 1.78 | 1.48 | |
LBUL_0392 | Aspartate/tyrosine/aromatic aminotransferase | 1.33 | 1.02 | 3.31 | 0.62 | |
LBUL_0431 | Branched-chain amino acid permease | 0.71 | 0.58 | 2.34 | 1.44 | |
LBUL_0659 | Valyl-tRNA synthetase | 1.08 | 0.43 | 1.27 | 6.46 | |
LBUL_0681 | Isoleucyl-tRNA synthetase | 0.94 | 0.62 | 1.74 | 4.51 | |
LBUL_1180 | Aspartate/tyrosine/aromatic aminotransferase | 1.15 | 1.21 | 0.51 | 1.13 | |
LBUL_1219 | BCAA aminotransferase/4-amino-4-deoxychorismate lyase | 0.64 | 0.63 | 0.56 | 4.74 | |
LBUL_1451 | Leucyl-tRNA synthetase | 0.86 | 0.41 | 0.87 | 3.54 | |
LBUL_2034 | Thiamine pyrophosphate-requiring enzymes [acetolactate synthase pyruvate dehydrogenase (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase] | 0.44 | 0.24 | 0.80 | 11.11 | |
str0220 | leuS | Leucyl-tRNA synthetase | 2.13 | 1.95 | 2.17 | 1.22 |
str0359 | livJ | BCAA ABC transporter substrate-binding protein | 1.37 | 0.80 | 1.30 | 0.60 |
str0360 | livH | BCAA ABC transporter permease protein | 1.18 | 0.76 | 1.33 | 0.79 |
str0361 | livM | BCAA ABC transporter permease protein | 1.09 | 0.67 | 1.34 | 1.22 |
str0362 | livG | BCAA ABC transporter ATP binding protein | 2.00 | 1.14 | 1.03 | 1.49 |
str0363 | livF | BCAA ABC transporter ATP binding protein | 1.51 | 0.62 | 0.96 | 1.37 |
str0477 | valS | Valyl-tRNA synthetase | 1.03 | 0.83 | 3.59 | 4.89 |
str0590 | bcaT | BCAA aminotransferase | 2.01 | 1.18 | 0.78 | 0.30 |
str0644 | hdhL | l-2-Hydroxyisocaproate dehydrogenase | 1.14 | 1.11 | 1.15 | 3.24 |
str0741 | ileS | Isoleucyl-tRNA synthetase | 0.81 | 0.86 | 2.18 | 2.63 |
str1357 | brnQ | BCAA transport system II carrier protein | 0.51 | 0.59 | 1.44 | 0.28 |
str1438 | amiF1 | Oligopeptide ABC transporter ATP-binding protein | 0.49 | 0.39 | 2.75 | 0.72 |
str1439 | amiE | Oligopeptide ABC transporter ATP-binding protein | 0.61 | 0.23 | 2.46 | 0.62 |
str1440 | amiD | Oligopeptide ABC transporter membrane-binding protein | 0.45 | 0.14 | 2.73 | 0.55 |
str1441 | amiC | Oligopeptide ABC transporter membrane-binding protein | 0.50 | 0.30 | 2.79 | 0.39 |
str1635 | codY | Transcriptional repressor CodY | 1.01 | 0.76 | 0.59 | 1.02 |
Sulfur amino acid metabolism | ||||||
LBUL_0089 | Homoserine trans-succinylase | 0.61 | 0.46 | 0.76 | 0.21 | |
LBUL_0096 | Methionine synthase II (cobalamin-independent) | 2.66 | 0.84 | 2.71 | 1.24 | |
LBUL_0268 | Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) | 2.48 | 0.79 | 3.03 | 0.93 | |
LBUL_0297 | Methionyl-tRNA synthetase | 1.81 | 0.91 | 1.11 | 2.24 | |
LBUL_0685 | Adenosyl homosysteine nucleosidase | 0.23 | 0.35 | 4.17 | 5.42 | |
LBUL_0686 | Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes | 0.41 | 0.34 | 1.14 | 5.14 | |
LBUL_1103 | Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities | 0.32 | 0.75 | 1.54 | 1.97 | |
LBUL_1232 | Methionine synthase II (cobalamin-independent) | 0.50 | 0.55 | 0.94 | 2.23 | |
LBUL_1235 | Cysteine synthase | 9.11 | 2.88 | 23.09 | 2.84 | |
LBUL_1236 | Cystathionine beta-lyases/cystathionine gamma-synthases | 6.30 | 2.85 | 13.94 | 4.31 | |
LBUL_1259 | Homoserine dehydrogenase | 0.93 | 0.93 | 1.84 | 1.02 | |
LBUL_1353 | Homoserine trans-succinylase | 0.50 | 0.27 | 0.59 | 0.08 | |
LBUL_1354 | Cysteine synthase | 0.69 | 0.21 | 0.36 | 0.03 | |
LBUL_1455 | S-Adenosylmethionine synthetase | 1.08 | 0.68 | 1.98 | 0.63 | |
LBUL_1554 | Cysteinyl-tRNA synthetase | 0.53 | 0.75 | 0.35 | 1.30 | |
str0083 | cysE1 | Serine acetyltransferase | 0.69 | 0.76 | 1.59 | 0.56 |
str0084 | cysS | Cysteinyl-tRNA synthetase | 0.79 | 0.74 | 1.86 | 0.73 |
str0352 | metB1 | Cystathionine gamma-synthase | 0.09 | 0.02 | 1.27 | 0.05 |
str0366 | cysM1 | Cysteine synthase | 0.44 | 0.10 | 0.88 | 0.31 |
str0451 | metG | Methionine-tRNA ligase | 1.12 | 0.83 | 1.33 | 0.37 |
str0566 | pfs | 5′-Methylthioadenosine/S-adenosylhomocysteine nucleosidase | 0.49 | 0.94 | 2.91 | 1.59 |
str0584 | mmuM | Homocysteine methyltransferase | 0.40 | 0.45 | 1.42 | 0.32 |
str0846 | cysM2 | Cysteine synthase | 1.73 | 0.69 | 1.56 | 0.42 |
str0847 | metB2 | Cystathionine beta-lyase | 1.17 | 0.68 | 0.91 | 0.86 |
str0848 | cysE2 | Serine acetyltransferase, putative | 1.48 | 0.61 | 1.53 | 1.13 |
str0987 | cysD | O-Acetylhomoserine sulfhydrylase | 0.28 | 0.20 | 3.24 | 0.09 |
str1172 | metK | S-Adenosylmethionine synthetase | 0.40 | 0.57 | 1.52 | 0.06 |
str1222 | metA | Homoserine O-succinyltransferase | 0.28 | 0.26 | 1.49 | 0.13 |
Other amino acid and carbon dioxide metabolism | ||||||
LBUL_1105 | Subtilisin-like serine protease prtB | 0.45 | 0.42 | 8.89 | 0.42 | |
str1658 | cah | Carbonate dehydratase | 15.75 | 3.73 | 0.71 | 0.92 |
ROS production and iron metabolism | ||||||
LBUL_2034 | Acetolactate synthase pyruvate dehydrogenase, (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase | 0.44 | 0.24 | 0.80 | 11.11 | |
LBUL_1241 | Translation initiation factor 2 (IF-2; GTPase) | 2.29 | 2.19 | 3.48 | 1.22 | |
LBUL_1955 | Dihydroorotate dehydrogenase | 0.94 | 1.04 | 2.60 | 1.10 | |
str1025 | fatB | Ferrichrome ABC transporter, substrate-binding protein | 0.83 | 0.90 | 4.34 | 0.59 |
str1026 | fatA | Ferrichrome ABC transporter, ATP-binding protein | 0.66 | 1.00 | 4.52 | 0.54 |
str1027 | fatC | Ferrichrome ABC transporter, permease protein | 0.74 | 0.96 | 3.95 | 0.34 |
str1028 | fatD | Ferrichrome ABC transporter, permease protein | 0.77 | 0.95 | 2.74 | 0.09 |
str0723 | dpr | Peroxide resistance protein, non-heme iron-containing ferritin | 1.48 | 0.76 | 0.35 | 1.22 |
str0724 | fur | Ferric transport regulator protein | 1.37 | 1.13 | 0.42 | 1.51 |
Fatty acid metabolism | ||||||
LBUL_0106 | 1-Acyl-sn-glycerol-3-phosphate acyltransferase | 1.37 | 0.53 | 3.13 | 1.40 | |
LBUL_0109 | 1-Acyl-sn-glycerol-3-phosphate acyltransferase | 0.63 | 0.62 | 4.76 | 0.91 | |
LBUL_0314 | Phosphopantetheinyl transferase (holo-ACP synthase) | 0.86 | 0.73 | 0.66 | 0.99 | |
LBUL_0818 | 3-Oxoacyl-(acyl-carrier-protein) | 1.67 | 0.37 | 0.26 | 0.20 | |
LBUL_0819 | Acyl carrier protein | 1.49 | 0.84 | 0.32 | 0.41 | |
LBUL_0820 | (Acyl-carrier-protein) S-malonyltransferase | 1.44 | 0.28 | 0.19 | 0.27 | |
LBUL_0821 | Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) | 1.66 | 0.33 | 0.26 | 0.20 | |
LBUL_0822 | 3-Oxoacyl-(acyl-carrier-protein) synthase | 1.68 | 0.33 | 0.22 | 0.22 | |
LBUL_0823 | Biotin carboxyl carrier protein | 0.97 | 0.41 | 0.21 | 0.34 | |
LBUL_0824 | 3-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases | 1.27 | 0.29 | 0.29 | 0.47 | |
LBUL_0825 | Acetyl/propionyl-CoAb carboxylase alpha subunit | 0.98 | 0.30 | 0.13 | 0.39 | |
LBUL_0826 | Acetyl-CoA carboxylase beta subunit | 0.94 | 0.28 | 0.24 | 0.28 | |
LBUL_0827 | Acetyl-CoA carboxylase alpha subunit | 1.36 | 0.26 | 0.60 | 0.37 | |
LBUL_0828 | Enoyl-(acyl-carrier-protein) | 0.90 | 0.30 | 0.10 | 0.32 | |
LBUL_0829 | Biotin-(acetyl-CoA carboxylase) ligase | 0.79 | 0.26 | 0.30 | 0.28 | |
LBUL_1256 | 1-Acyl-sn-glycerol-3-phosphate acyltransferase | 1.09 | 0.35 | 1.55 | 14.99 | |
LBUL_1294 | Acyl carrier protein | 0.88 | 1.00 | 0.29 | 1.78 | |
LBUL_1356 | Cyclopropane fatty acid synthase and related methyltransferases | 0.77 | 0.41 | 0.52 | 0.05 | |
LBUL_1567 | Biotin carboxylase | 1.64 | 0.98 | 3.59 | 0.76 | |
LBUL_1568 | Biotin carboxylase | 0.88 | 0.49 | 1.29 | 0.36 | |
LBUL_1607 | 3-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases | 0.60 | 0.44 | 0.71 | 4.36 |
Numbers indicate the ratios of differential expression of a gene in the mixed culture compared to the monoculture. Numbers in boldface have a ratio >2 or <0.5 and are significant (P = 0.05).
CoA, coenzyme A.